Why all this contortion to fit this and AvP (of all films) into some grand plot. Do you think Ridley Scott really cares for what any AvP or any film maker did of the alien sequels?
I have no idea what Ridley Scott cares for.
Of course there's almost always contradictions in a long running series like this, but part of the fun is inventing ways to explain them. This may be "fanwank", but so what.
Even if Peter Weyland is explained as being the head *and the founder* of Weyland Industries, that's not necessarily a contradiction. Peter's obviously got one hell of an ego, so he probably just downplayed Charles' existence altogether and made himself look more important. I'm sure that happens a lot in real life corporations.